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Bug #1224

Possible numerical overflow in mdrun -nsteps (or its output to the log file and stderr)

Added by Chris Neale about 4 years ago. Updated over 3 years ago.

Status:
Closed
Priority:
Low
Assignee:
Category:
mdrun
Target version:
-
Affected version - extra info:
4.6
Affected version:
Difficulty:
uncategorized
Close

Description

I made a .tpr using 4.6.1 with nsteps = 5000000 in the mdp file.
I then ran:
mdrun -nsteps 5000000000

However, the .log file indicates:
Overriding nsteps with value passed on the command line: 705032704 steps, 1410065.408 ps

And the stderr reports:
-nsteps int 705032704 Run this number of steps, overrides .mdp file
option
Overriding nsteps with value passed on the command line: 705032704 steps, 1410065.408 ps
Using 72 MPI processes
WARNING: This run will generate roughly 4103 Mb of data
903042024 steps, 1806084.0 ps (continuing from step 198009320, 396018.6 ps).

Associated revisions

Revision 08180bb0 (diff)
Added by Berk Hess about 4 years ago

changed mdrun -nsteps to gmx_large_int_t

Fixes #1224

Change-Id: Idc66a0de4b8c6463be2df92ee7b8261a90eb5014

Revision cfc8751d (diff)
Added by Berk Hess about 4 years ago

changed mdrun -nsteps to gmx_large_int_t

Fixes #1224

Change-Id: Idc66a0de4b8c6463be2df92ee7b8261a90eb5014

History

#1 Updated by Berk Hess about 4 years ago

  • Status changed from New to In Progress

Several years ago I changed all our internal step variables to 64 bits (if supported).
But there is no 64 bit integer command line option.
If possible, you could use mdrun -nsteps -1
We will need to introduce a 64 bit integer command line option or we could read it from a string, but that might be confusing.

#2 Updated by Berk Hess about 4 years ago

  • Status changed from In Progress to Feedback wanted
  • Affected version - extra info set to 4.6

We do already have a large int command line option.
Could you please check that my fix works?
https://gerrit.gromacs.org/#/c/2334/

#3 Updated by Chris Neale about 4 years ago

Yes, thank you Berk, this now reports the value correctly:

Original:
$ ~/exe/gromacs-4.6.1/exec/bin/mdrun -nt 1 -notunepme -deffnm md3 -dlb yes -npme -1 -cpt 60 -maxh 0.1 -cpi md3.cpt -nsteps 5000000000 -v
Overriding nsteps with value passed on the command line: 705032704 steps, 1410065.408 ps

Your new modification:
$ ~/exe/4.6.1_berkfix/exec/bin/mdrun -nt 1 -notunepme -deffnm md3 -dlb yes -npme -1 -cpt 60 -maxh 0.1 -cpi md3.cpt -nsteps 5000000000 -v
Overriding nsteps with value passed on the command line: 5000000000 steps, 10000000.000 ps

#4 Updated by Berk Hess about 4 years ago

  • Status changed from Feedback wanted to Resolved
  • % Done changed from 0 to 100

#5 Updated by Anonymous about 4 years ago

#6 Updated by Anonymous about 4 years ago

#8 Updated by Rossen Apostolov over 3 years ago

  • Status changed from Resolved to Closed
  • Affected version set to 4.6

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